mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 702,330 | Δ1 bp | 22.2% | coding (422/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 1,158,383 | G→A | 13.7% | W172* (TGG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC JC | 1,159,287 | IS2 (–) +5 bp | 60.2% | coding (1419‑1423/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,466,438 | T→G | 5.9% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,712 | G→A | 5.8% | pseudogene (1321/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,714 | T→C | 6.6% | pseudogene (1323/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,717 | C→T | 8.7% | pseudogene (1326/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 6.4% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,708,709 | T→C | 9.5% | R597R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,726,155 | T→G | 55.2% | F45V (TTC→GTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,373 | Δ1 bp | 16.7% | coding (351/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,374 | Δ1 bp | 16.7% | coding (352/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| JC | 1,726,492 | Δ4 bp | 17.6% | coding (470‑473/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,528 | G→T | 7.4% | G169V (GGC→GTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,570:1 | +G | 7.5% | coding (548/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,233,246 | T→G | 10.4% | F528V (TTC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,529 | C→G | 6.3% | S31C (TCC→TGC) | yidX → | putative lipoprotein |
| RA | 3,875,536 | C→A | 8.8% | T33T (ACC→ACA) | yidX → | putative lipoprotein |
| MC JC | 3,909,312 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,171,648 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 6.9% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 26.0% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 23.2% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 23.4% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,088 | T→G | 6.2% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| JC | 4,606,167 | Δ236 bp | 5.1% | leuP–leuQ | leuP, leuQ | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4110687 | 4111551 | 865 | 63 [61] | [61] 63 | tpiA | tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225456 = | 70 (0.480) | 5 (0.040) | 5/502 | NT | 5.7% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | 4037237 = | 97 (0.700) | intergenic (+20/‑23) | ileT/alaT | tRNA‑Ile/tRNA‑Ala | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 3 (0.020) | 3/506 | NT | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 1207790 = | 53 (0.370) | 83 (0.610) | 60/488 | NT | 64.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 42 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207794 | 55 (0.380) | 3 (0.020) +G |
3/518 | NT | 5.8% | coding (294/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209612 | 43 (0.300) | pseudogene (8/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 53 (0.370) | 86 (0.630) | 57/488 | NT | 65.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 42 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 81 (0.570) | 61/512 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||